NuPoP

DOI: 10.18129/B9.bioc.NuPoP    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see NuPoP.

An R package for nucleosome positioning prediction

Bioconductor version: 3.13

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at http://nucleosome.stats.northwestern.edu.

Author: Ji-Ping Wang <jzwang at northwestern.edu>; Liqun Xi <liqunxi02 at gmail.com>; Oscar Zarate <zarate at u.northwestern.edu>

Maintainer: Ji-Ping Wang<jzwang at northwestern.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NuPoP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NuPoP")

 

HTML	R Script	NuPoP
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Genetics, HiddenMarkovModel, NucleosomePositioning, Software, Visualization
Version	2.0.0
In Bioconductor since	BioC 2.7 (R-2.12) (11 years)
License	GPL-2
Depends	R (>= 4.0)
Imports	graphics, utils
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	nuCpos
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	NuPoP_2.0.0.tar.gz
Windows Binary	NuPoP_2.0.0.zip
macOS 10.13 (High Sierra)	NuPoP_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NuPoP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NuPoP
Package Short Url	https://bioconductor.org/packages/NuPoP/
Package Downloads Report	Download Stats